From 11f01f92cd17c5c975978db69e31cada0084c0b9 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 3 Aug 2015 11:19:19 +0200
Subject: [PATCH] Review changes to kraken
---
.../biopet/extensions/kraken/Kraken.scala | 61 ++++++++-----------
1 file changed, 26 insertions(+), 35 deletions(-)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
index 89d72249a..da53b6841 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/kraken/Kraken.scala
@@ -28,6 +28,15 @@ class Kraken(val root: Configurable) extends BiopetCommandLineFunction {
@Input(doc = "Input: FastQ or FastA")
var input: List[File] = _
+ @Output(doc = "Unidentified reads", required = false)
+ var unclassified_out: Option[File] = None
+
+ @Output(doc = "Identified reads", required = false)
+ var classified_out: Option[File] = None
+
+ @Output(doc = "Output with hits per sequence")
+ var output: File = _
+
var db: File = config("db")
var inputFastQ: Boolean = true
@@ -36,55 +45,37 @@ class Kraken(val root: Configurable) extends BiopetCommandLineFunction {
var compressionBzip: Boolean = false
var quick: Boolean = false
- var min_hits: Option[Int] = config("min_hits")
-
- @Output(doc = "Unidentified reads", required = false)
- var unclassified_out: Option[File] = None
- @Output(doc = "Identified reads", required = false)
- var classified_out: Option[File] = None
+ var minHits: Option[Int] = config("min_hits")
- @Output(doc = "Output with hits per sequence")
- var output: File = _
- var preload: Boolean = config("preload", default = true)
+ var preLoad: Boolean = config("preload", default = true)
var paired: Boolean = config("paired", default = false)
executable = config("exe", default = "kraken")
override def versionRegex = """Kraken version ([\d\w\-\.]+)\n.*""".r
override def versionExitcode = List(0, 1)
+ override def versionCommand = executable + " --version"
override def defaultCoreMemory = 8.0
override def defaultThreads = 4
- override def versionCommand = executable + " --version"
-
/** Sets readgroup when not set yet */
override def beforeGraph(): Unit = {
super.beforeGraph()
+ //FIXME: This does not do anything
}
/** Returns command to execute */
- def cmdLine = {
- var cmd: String = required(executable) +
- "--db" + required(db) +
- optional("--threads", nCoresRequest) +
- conditional(inputFastQ, "--fastq-input") +
- conditional(!inputFastQ, "--fasta-input") +
- conditional(quick, "--quick")
-
- min_hits match {
- case Some(v) => cmd += "--min_hits " + v
- case _ => cmd += ""
- }
-
- cmd += optional("--unclassified-out ", unclassified_out.get) +
- optional("--classified-out ", classified_out.get) +
- "--output" + required(output) +
- conditional(preload, "--preload") +
- conditional(paired, "--paired")
-
- // finally the input files (R1 [R2])
- cmd += input.mkString(" ")
-
- cmd
- }
+ def cmdLine = required(executable) +
+ "--db" + required(db) +
+ optional("--threads", nCoresRequest) +
+ conditional(inputFastQ, "--fastq-input") +
+ conditional(!inputFastQ, "--fasta-input") +
+ conditional(quick, "--quick") +
+ optional("--min_hits", minHits) +
+ optional("--unclassified-out ", unclassified_out.get) +
+ optional("--classified-out ", classified_out.get) +
+ "--output" + required(output) +
+ conditional(preLoad, "--preload") +
+ conditional(paired, "--paired") +
+ repeat(input)
}
--
GitLab